The Forest Temple was well made, and probably would be my favourite if it wasn't QUITE so well made - the atmosphere and music are just so damn creepy that they seep into your pores and make you all claustrophobic, particularly when you're running around for hours looking for a key which turns out to be hidden up a tree in an antechamber you don't think is actually PART of the temple, so you're just stuck, frantically searching while the music loops on... But really, if it wasn't for that, I probably would've enjoyed that dungeon the most.
So, discounting that, I'd have to go for... Snowpeak Ruins or Mansion or whatever in Twilight Princess. I just found the environment really neat, not something you often come across in a Zelda game. And the music was great too, but really, you can say that for MOST of anything Legend of Zelda.